Contacts of the helix formed by residues 170 - 183 (chain B) in PDB entry 4X4W
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ASP* 3.0 16.5 + - - +
169B TYR* 1.3 76.6 - - - +
171B ARG* 1.3 56.8 + - - +
173B LEU* 2.9 30.6 + - + -
174B ARG* 3.1 19.7 + - + +
204B LEU* 4.1 5.8 - - + -
207B ILE* 4.1 15.0 - - + +
211B ARG* 3.3 57.0 - - + +
212B ILE* 4.0 15.9 - - + -
215B GLU* 4.0 23.8 - - + +
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ARG 4.1 7.1 + - - -
126B ASP* 3.7 35.0 + - + +
157B PHE* 4.1 22.5 - - + -
164B ARG* 3.0 48.4 + - - +
165B ILE* 4.5 6.7 - - - -
167B GLU* 2.9 33.5 + - - +
168B ASP* 2.9 31.9 + - + +
170B LEU* 1.3 74.1 - - - +
172B ILE* 1.3 57.6 + - - +
173B LEU 3.3 0.2 - - - -
174B ARG* 3.7 12.1 - - - +
175B TYR* 2.9 28.6 + - - +
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ILE* 3.8 30.5 - - + +
169B TYR* 3.0 20.4 + - + +
171B ARG* 1.3 77.9 - - - +
173B LEU* 1.3 64.7 + - + +
175B TYR* 3.3 14.8 + - - +
176B PHE* 3.3 27.9 + - + -
197B ILE* 3.7 32.1 - - + +
200B ASN* 3.7 31.9 - - + +
201B ALA* 3.9 10.1 - - + -
204B LEU* 3.9 21.8 - - + -
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 2.9 22.9 + - + +
172B ILE* 1.3 77.7 - - + +
174B ARG* 1.3 60.6 - - - +
176B PHE* 3.2 24.8 + - + +
177B ARG* 2.9 28.8 + - - +
204B LEU* 4.4 18.2 - - + -
212B ILE* 4.0 39.5 - - + +
215B GLU* 4.0 18.2 - - + -
216B LEU* 4.6 9.6 - - + +
219B ILE* 3.6 12.9 - - + +
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP* 2.8 33.0 + - - +
127B LEU* 4.9 2.7 - - + -
130B ASN* 3.7 10.5 - - - +
168B ASP* 5.8 2.5 - - - -
170B LEU* 3.1 21.2 + - + +
171B ARG* 3.7 18.8 - - + +
172B ILE 3.3 0.2 - - - -
173B LEU* 1.3 74.0 - - - +
175B TYR* 1.3 66.5 + - - +
177B ARG* 3.3 22.1 + - - +
178B PHE* 3.0 59.4 + - + -
211B ARG* 6.1 0.2 - - - +
215B GLU* 3.7 27.0 + - + -
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Residues in contact with TYR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 4.8 4.7 - - + +
155B VAL* 3.5 49.5 + - + +
157B PHE* 4.5 15.0 - + + -
171B ARG 2.9 15.0 + - - +
172B ILE* 3.5 8.3 - - - +
173B LEU 3.2 0.2 - - - -
174B ARG* 1.3 77.0 - - - +
176B PHE* 1.3 72.6 + + - +
178B PHE* 3.4 0.5 + - - -
179B TYR* 2.9 41.7 + + + +
189B HIS* 2.7 42.9 + + - +
190B ASP* 4.6 2.6 + - + +
193B THR* 3.9 22.3 - - + +
194B LEU* 4.4 4.1 - - + +
197B ILE* 3.5 30.1 - - + -
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Residues in contact with PHE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ILE* 3.3 31.1 + - + -
173B LEU* 3.2 24.7 + - + +
175B TYR* 1.3 97.8 - + - +
177B ARG* 1.3 63.7 + - - +
179B TYR* 3.3 2.3 + - - +
180B GLY 3.0 19.1 + - - -
189B HIS* 5.8 3.8 - + - -
194B LEU* 5.5 4.5 - - + -
197B ILE* 4.0 25.1 - - + -
219B ILE* 4.0 11.4 - - + -
228B LEU* 3.1 47.4 - - + +
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Residues in contact with ARG 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ARG* 4.7 7.1 - - - +
173B LEU 2.9 16.6 + - - +
174B ARG* 3.6 21.0 - - - +
175B TYR 3.3 0.2 - - - -
176B PHE* 1.3 76.9 - - - +
178B PHE* 1.3 86.5 + - + +
180B GLY* 3.4 2.9 + - - -
181B ARG* 3.0 33.8 + - + +
215B GLU* 3.0 35.8 + - - +
218B LYS* 3.5 46.9 - - + +
219B ILE* 3.8 19.0 - - + +
228B LEU* 4.7 1.9 - - - +
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Residues in contact with PHE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ARG* 3.2 48.9 - - - -
127B LEU* 3.6 26.7 - - + -
129B ILE* 4.3 8.3 - - + -
130B ASN* 3.4 15.9 - - - -
155B VAL* 4.0 7.9 - - + -
174B ARG* 3.0 52.7 + - + +
175B TYR 4.2 1.1 - - - +
177B ARG* 1.3 112.1 - - + +
179B TYR* 1.3 64.3 + - - +
181B ARG* 3.5 13.3 - - + +
182B ILE* 3.1 29.2 + - + +
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LYS 5.4 1.8 - - - -
155B VAL* 3.7 19.4 - - + +
175B TYR* 2.9 37.1 + - + +
176B PHE* 3.6 7.2 - - - +
178B PHE* 1.3 77.2 - - - +
180B GLY* 1.3 65.0 + - - +
183B VAL* 3.1 61.9 + - + +
186B PRO* 3.7 7.6 - - + +
187B GLY 3.0 22.2 + - - -
188B ASP* 2.7 30.1 + - - +
189B HIS* 3.2 31.6 + + - -
224B HIS* 6.0 1.8 - + + -
227B HIS* 3.8 12.3 - + - -
228B LEU* 4.1 11.9 - - + -
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Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B PHE 3.0 12.3 + - - -
177B ARG 3.8 3.6 - - - -
179B TYR* 1.3 79.3 - - - +
181B ARG* 1.3 60.4 + - - +
183B VAL 4.1 2.3 - - - +
223B ASN* 3.4 43.4 + - - +
224B HIS* 3.5 16.8 - - - -
228B LEU* 3.9 11.2 - - - +
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Residues in contact with ARG 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ARG* 3.8 20.7 - - - +
42B ASP* 2.7 31.2 + - - -
45B ASN* 5.4 8.2 + - - +
47B VAL* 5.0 14.8 - - - +
177B ARG* 3.0 24.4 + - + +
178B PHE* 3.5 22.2 - - + +
179B TYR 3.1 0.6 - - - -
180B GLY* 1.3 80.1 - - - +
182B ILE* 1.3 68.9 + - + +
183B VAL 5.1 0.2 - - - +
223B ASN* 4.7 14.0 + - - +
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Residues in contact with ILE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ARG* 4.5 4.5 - - - -
45B ASN* 4.0 25.2 + - - +
129B ILE* 4.0 20.0 - - + -
150B LEU* 4.0 21.1 - - + +
153B LYS* 3.6 46.7 - - + +
154B LYS 3.9 7.9 - - - +
155B VAL* 3.7 24.2 - - + -
178B PHE* 3.1 18.4 + - - +
181B ARG* 1.3 87.5 - - + +
183B VAL* 1.3 71.5 + - + +
184B ASP* 3.7 2.6 + - - +
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LYS* 3.8 27.8 - - + +
155B VAL* 4.7 0.4 - - + -
179B TYR* 3.1 54.9 + - + +
180B GLY 4.1 2.3 - - - +
181B ARG 3.8 0.4 - - - -
182B ILE* 1.3 87.0 - - + +
184B ASP* 1.3 66.9 + - - +
185B LYS 3.6 27.1 - - - +
186B PRO* 4.0 10.1 - - + -
223B ASN* 5.8 0.2 + - - -
224B HIS* 3.0 23.7 + - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il